Monday, June 4, 2012

The Epicureans called them “veering atoms” and evolutionists updated it to “random mutations.” One way or another, man must have an evolutionary narrative. But it makes no sense on the science and so, to match the mythology with the evidence, evolution must become the master craftsman. Its latest wizardry is a “risk management strategy,” as a new paper explains. Furthermore, mutation rates have been “evolutionarily optimized.” Unbelievable. The evolutionist’s just-so stories continue to become even more ridiculous. Evolution is now so brilliant that we are supposed to believe that it created the means not only to control mutation rates, but to optimize the mutation rates as well.

First, if evolution is true, we must believe that the basic mutation rate varies by more than an order of magnitude in different bacteria:

Upon comparing 34 Escherichia coli genomes, we observe that the neutral mutation rate varies by more than an order of magnitude across 2,659 genes, with mutational hot and cold spots spanning several kilobases.

The next result is that, under evolution, the variation between different mutation rates must not be random, but rather must follow a rational pattern:

Importantly, the variation is not random: we detect a lower rate in highly expressed genes and in those undergoing stronger purifying selection.

And so, given evolution, we must conclude that evolution has optimized the mutation rate:

Our observations suggest that the mutation rate has been evolutionarily optimized to reduce the risk of deleterious mutations.

Of course there is no known mechanism that could do this:

Current knowledge of factors influencing the mutation rate—including transcription-coupled repair and context-dependent mutagenesis—do not explain these observations, indicating that additional mechanisms must be involved.

But evolutionists will think of something, no matter how speculative.

The findings have important implications for our understanding of evolution and the control of mutations.

In other words, results that rebuke a fundamental concept of evolution, and that cannot even be explained by evolutionists (who are notorious for being able to explain anything with their just-so stories), are presented by evolutionists as important findings for understanding how evolution works. It is all about those veering atoms.

113 comments:

If you trace the source for entropic randomness down in the universe you find out some very interesting things:

Being the helpful guy I am, always trying to help atheists out when I get a chance, I’ve been trying to piece together a experiment that would prove once and for all, for everyone to see, that RANDOM variation plus undirected natural selection can produce functional proteins just as atheists adamantly claim (even though no one has ever seen RANDOM processes do this). Now I just about got the RANDOM part of the experiment down for the atheists! I’ve searched for the maximum source of randomness that I could find in the universe, (since the 'god of randomness' is who atheists adamantly claim for their creator), and I think I’ve found their god for them;

First:

Evolution is a Fact, Just Like Gravity is a Fact! UhOh! - January 2010Excerpt: The results of this paper suggest gravity arises as an entropic force, once space and time themselves have emerged.http://www.uncommondescent.com/intelligent-design/evolution-is-a-fact-just-like-gravity-is-a-fact-uhoh/

Thermodynamics – 3.1 EntropyExcerpt:Entropy – A measure of the amount of randomnessor disorder in a system.http://www.saskschools.ca/curr_content/chem30_05/1_energy/energy3_1.htm

Thus, the more entropy a system has the more randomness it will generate for our experiment to find a RANDOM functional protein. And if we ask, ‘what is the maximum source of entropy, i.e. RANDOMNESS, in the universe?’, we find this:

Entropy of the Universe – Hugh Ross – May 2010Excerpt: Egan and Lineweaver found that supermassive black holes are the largest contributor to the observable universe’s entropy. They showed that these supermassive black holes contribute about 30 times more entropy than what the previous research teams estimated.http://www.reasons.org/entropy-universe

“But why was the big bang so precisely organized, whereas the big crunch (or the singularities in black holes) would be expected to be totally chaotic? It would appear that this question can be phrased in terms of the behaviour of the WEYL part of the space-time curvature at space-time singularities. What we appear to find is that there is a constraint WEYL = 0 (or something very like this) at initial space-time singularities-but not at final singularities-and this seems to be what confines the Creator’s choice to this very tiny region of phase space.”Roger Penrose - How Special Was The Big Bang?

Plus for a added bonus for atheists, being the helpful guy that I am, I found that if we find a massive magnetized blackhole we might just start to overcome the homochirality problem, which is a huge problem against finding functional proteins, as well:

Homochirality and Darwin: part 2 – Robert Sheldon – May 2010Excerpt: With regard to the deniers who think homochirality is not much of a problem, I only ask whether a solution requiring multiple massive magnetized black-hole supernovae doesn’t imply there is at least a small difficulty to overcome? A difficulty, perhaps, that points to the non-random nature of life in the cosmos?http://procrustes.blogtownhall.com/page3

But of course there is the extreme logistics problem with actually transporting the atheists to the massive magnetized blackholes to actually do the experiments, so that they may try to actually RANDOMLY generate a functional protein just as they claim can be done. Not to mention the minor problem of someone trying to survive being stretched into as a piece of spaghetti, by the extreme warping of space-time, near the blackhole.What Would Happen If You Fell into a Black Hole? - videohttp://www.youtube.com/watch?v=gLMiJQXsmkc

,,Not to mention trying to survive the extremely high temperatures surrounding the event horizon of the black hole:,,

Scientists gear up to take a picture of a black hole - January 2012Excerpt: "Swirling around the black hole like water circling the drain in a bathtub, the matter compresses and the resulting friction turns it into plasma heated to a billion degrees or more, causing it to 'glow' – and radiate energy that we can detect here on Earth."http://www.physorg.com/news/2012-01-scientists-gear-picture-black-hole.html

But what the hey, it is just a little sacrifice for ‘science’ right!?! At least atheists will have the maximum source of randomness in the universe to work with in their experiments!!! But there is another problem I probably need to tell atheists about before they pack up and go off to the massive magnetized blackholes in order to prove to the world that their ‘god of randomness’ can create all things,

“Is there a real connection between entropy in physics and the entropy of information? ….The equations of information theory and the second law are the same, suggesting that the idea of entropy is something fundamental…”Tom Siegfried, Dallas Morning News, 5/14/90 – Quotes attributed to Robert W. Lucky, Ex. Director of Research, AT&T, Bell Laboratories & John A. Wheeler, of Princeton & Univ. of TX, Austin in the articlehttp://www.bible.ca/tracks/dp-lawsScience.htm

But what the hey, atheists haven't needed any stinking equations to prove their theory so far have they!?!

Oxford University Admits Darwinism's Shaky Math Foundation - May 2011Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. - On a 2011 Job Description for a Mathematician, at Oxford, to 'fix' the persistent mathematical problems with neo-Darwinism within two years.http://www.evolutionnews.org/2011/05/oxford_university_admits_darwi046351.html

I even have a inspirational quote for the future experiment of our space traveling atheists;

GILBERT NEWTON LEWIS: AMERICAN CHEMIST (1875-1946)“I have attempted to give you a glimpse…of what there may be of soul in chemistry. But it may have been in vain. Perchance the chemist is already damned and the guardian the blackest. But if the chemist has lost his soul, he will not have lost his courage and as he descends into the inferno, sees the rows of glowing furnaces and sniffs the homey fumes of brimstone, he will call out-: ‘Asmodeus, hand me a test-tube.’”(1) Gilbert Newton Lewishttp://www.woodrow.org/teachers/ci/1992/Lewis.html

Were you around to see how gravity arose? Were the authors? Sounds like another physics 'just-so' story to me.

Gravity is still a fact, though. Trip over your own feet and you will soon find out how much.

It's the same for evolution. There's no doubt that living things change over time. How that happens is still being investigated - by some, at least. Those who want more than just "God did it", that is.

Although neo-Darwinists are infamous for claiming that Darwinian evolution is as well established as gravity. This claim is false! For one thing Gravity, as formulated within General Relativity, can be falsified:

The happiest thought of my life.Excerpt: Then the Principle of Equivalence states that'the inertial and gravitational masses are identical.'The whole of the General Theory of Relativity rests on this postulate, and will fail if one can find a material for which the inertial and gravitational masses have different values.http://physics.ucr.edu/~wudka/Physics7/Notes_www/node85.html

Whereas, neo-Darwinism has no identifiable falsification criteria:

Science and Pseudoscience – Imre Lakatos“nobody to date has yet found a demarcation criterion according to which Darwin can be described as scientific” – Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, , quote as stated in 1973 LSE Scientific Method Lecture

Moreover, Gravity, as formulated within General Relativity, has been confirmed to stunning degree of accuracy:

Einstein’s General Relativity Tested Again, Much More Stringently - 2010Excerpt: As Müller puts it, “If the time of freefall was extended to the age of the universe – 14 billion years – the time difference between the upper and lower routes would be a mere one thousandth of a second, and the accuracy of the measurement would be 60 ps, the time it takes for light to travel about a centimetre.”http://www.universetoday.com/56612/einsteins-general-relativity-tested-again-much-more-stringently/

Whereas neo-Darwinists have yet to demonstrate that even a single protein can arise by purely material processes:

Moreover besides a strong case now being made that Gravity, as described by General Relativity, arises as a entropic force, as measured by 'chaotic randomness', there is also a very strong case to be made that the cosmological constant in General Relativity, the expansion of space-time, drives, or is deeply connected to, entropy as measured by diffusion:

Big RipExcerpt: The Big Rip is a cosmological hypothesis first published in 2003, about the ultimate fate of the universe, in which the matter of universe, from stars and galaxies to atoms and subatomic particles, are progressively torn apart by the expansion of the universe at a certain time in the future. Theoretically, the scale factor of the universe becomes infinite at a finite time in the future.http://en.wikipedia.org/wiki/Big_Rip

Thus though neo-Darwinian atheists may claim that evolution is as well established as Gravity, the plain fact of the matter is that General Relativity itself, which is by far our best description of Gravity, testifies strongly against neo-Darwinism.

Poor Cornelius. It must gnaw at your insides something terrible to see real scientists doing real research and publishing results in real science journals. All the while you hide on the sidelines with your Creationist buddies doing zero point squat and watch the scientific world pass you by.

Do you ever wonder about your science career that might have been? There's a big wonderful world out there with a million new things to explore, but all you can do is sit on your duff and mock the hard work of others. I feel sorry you, I really do.

I have never seen Hunter mocks the work of others. On the contrary, he promotes such work. Hunter only mocks the silly habits of evolutionists who feel compelled to force-fit scientific biological data into the Darwinist evolutionary mold whether or not there is a fit. It's laughable.

Thanks for the paid ad-hom, I'll add it to the box I keep useless verbiage in. Still I suppose it was the best reasoning you could come up with. Just waiting for our lady friend to say "But Cornelius, we already knew that" :-P

So Thorton, since the driving force for adaptations, in this paper and numerous other papers, is shown to be 'non-random', and yet neo-Darwinism requires RANDOM variation as the primary driving force for Darwinian evolution, what does the 'science' itself indicate?

notes:

Revisiting the Central Dogma in the 21st Century - James A. ShapiroExcerpt: Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, Genome change arises as a consequence of natural genetic engineering, not from accidents,,, Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome,,,http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf

Moreover Thorton, it is just not the random variation part of neo-Darwinism that is falsified as a driving force for Darwinism. Natural selection itself also falls apart upon scrutiny,,

“Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. Quarter-power scaling laws are perhaps as universal and as uniquely biological as the biochemical pathways of metabolism, the structure and function of the genetic code and the process of natural selection.,,, The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection." Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79

Thorton, I really don't see how you can sit here Day after Day and pretend that Darwinism is not intellectually bankrupt.,,, But at least you do accomplish one good thing. You drive Dr. Hunter's point home of Darwinists being driven by their 'religion' rather than being driven by the evidence.

Thanks for the paid ad-hom, I'll add it to the box I keep useless verbiage in. Still I suppose it was the best reasoning you could come up with. Just waiting for our lady friend to say "But Cornelius, we already knew that"

That must be the same box you keep all of this disingenuous Creationist propaganda in.

I notice that neither you nor Hunter nor any of the other Creationist here could offer a single technical critique of the paper, or tell us what the authors got wrong. As always it's just a big steaming pile of personal incredulity: "ToE is so stupid!! ToE is so unbelievable!! Those authors must be incompetent frauds!!"

That's exactly why you Creationist "scientists" get laughed at by the real scientific community.

It's got to be a bit discouraging to be an evolutionist. The more you discover, the more you realize that you have to explain, meaning the hole you are trying to dig yourself out of just got deeper. And that seems to be the normal patter for scientific discoveries.

We applaud the research, the hard work, and the discoveries of evolutionists, but we find it difficult to accept the evolutionary interpretation of these discoveries that get passed off as science.

At some point you would think that there will be enough evidence to point towards an intelligent designer.

Atheistic evolutionists think there is enough evidence to support their views. Fine. They are welcome to their opinion.

Interpreted through a different lens, we think there is enough evidence to support the idea of intelligence being involved in creation of the universe and life.

Given that atheists rule out the involvement of any intelligence a priori, and given that this view cannot be proven, then obviously, they can never know if their conclusions and interpretation of the data are trustworthy or not. They too must take certain things by faith to come up with their views.

Tjguy: It's got to be a bit discouraging to be an evolutionist. The more you discover, the more you realize that you have to explain, meaning the hole you are trying to dig yourself out of just got deeper. And that seems to be the normal patter for scientific discoveries.

This is yet another example of a pre-enlightemnet, authoritative, static view of human knowledge.

The thing is, when there are new things to explain, this means we've made progress. Answers lead to new questions, which lead to even better answers, which lead to even better questions, etc. That's how science works.

So, no. It's not discouraging. It's encouraging.

What would be discouraging if we stopped discovering new questions to answer. In fact, this essentially represented the state of the human race for hundreds of thousands of years. For the most part, nothing changed over the span of many generations.

We explain our relatively recent and rapid increate in the creation of knowledge in that we've moved away from the sort of pre-enightment, authoritative conceptions human knowledge you seem to prefer.

TJGuy: We applaud the research, the hard work, and the discoveries of evolutionists, but we find it difficult to accept the evolutionary interpretation of these discoveries that get passed off as science.

Of course you would. That's because you hold an authoritative, justificationist conception of human knowledge.

This is the same conception behind the argument that there would be no knowledge of morality unless God told us what was right and wrong. It's essentially the same argument, in that there would be no life unless the designer put the knowledge found of how to build biological features in the genome.

Both of these arguments are based on the same flawed, authoritative conception of human knowledge.

TJGuy: Interpreted through a different lens, we think there is enough evidence to support the idea of intelligence being involved in creation of the universe and life.

Can you be any more vague?

TJGuy: Given that atheists rule out the involvement of any intelligence a priori, and given that this view cannot be proven, then obviously, they can never know if their conclusions and interpretation of the data are trustworthy or not. They too must take certain things by faith to come up with their views.

Unless you have a solution to the problem of induction, nothing can be proven in the sense you're referring to. At best, we can create explanations via conjecture, test those explanations using observations and discard those with errors.

Of course, if you have a solution to the problem of induction, then I'm all ears. I won't be holding my breath.

Our observations suggest that the mutation rate has been evolutionarily optimized to reduce the risk of deleterious mutations.

Cornelius Hunter: Of course there is no known mechanism that could do this

Not sure why you say that. Many of the repair mechanisms show signs of diversifying from a minimal set of primordial genes, and as for how repairs are implemented, there is an obvious evolutionary advantage to protecting critical genes at the expense of others.

Cornelius Hunter: Of course there is no known mechanism that could do this

Zachriel: Not sure why you say that.

Because he holds a pre-enlightenment, justificationist, authoritative conception of human knowledge.

We have knowledge of what is right and wrong because God told us.

Organisms have the knowledge of how to build adaptations because God put that knowledge in the cell. No designer, no knowledge, no adaptations, no life. Yet there is life, so there must have been a designer.

Cornelius, does that about sum it up?

Evolution is unlikely? But that assumes an absurd amount of knowledge would have "accidentally" or "spontaneously" appeared since knowledge can only come about though authoritative supernatural agents.

As such, It would come as no surprise that you'd think it's absurd.

Again, this can be explained that you hold a pre-enlightenment, justificationist, authoritative conception of human knowledge.

Blas: Scott can you explain wich is the right (obviuously yours) post enlightenment conception of human knowledge. Please be specific.

You're assuming we both concerned about the same thing. But, we're not.

From the following paper…

http://www.the-rathouse.com/Bartley/Leeson-vol.html

True believers embrace justificationism. They insist that some positions are better than others though they accept that there is no logical way to establish a positive justification for an belief. They accept that we make our choice regardless of reason: "Here I stand!". Most forms of rationalism up to date have, at rock bottom, shared this attitude with the irrationalists and other dogmatists because they share the theory of justificationism.

According to the critical rationalists, the exponents of critical preference, no position can be positively justified but it is quite likely that one (or more) will turn out to be better than others in the light of critical discussion and tests. This type of rationality holds all its positions and propositions open to criticism and a standard objection to this stance is that it is empty; just holding our positions open to criticism provides no guidance as to what position we should adopt in any particular situation. This criticism misses its mark for two reasons. First, critical rationalism is not a position. It is not directed at solving the kind of problems that are solved by fixing on a position. It is concerned with the way that such positions are adopted, criticized, defended and relinquished. Second, Bartley did provide guidance on adopting positions; we may adopt the position that to this moment has stood up to criticism most effectively. Of course this is no help for people who seek stronger reasons for belief, but that is a problem for them, and it does not undermine the logic of critical preference.

So, essentially, you keep asking me to be a justificationist, despite having pointed out that I'm not. Again, this sort of response indicates you're simply unable to recognize your conception of human knowledge as an idea that would be subject to criticism.

As a critical rationalist, I'm concerned with the way positions are adopted, criticized, defended and relinquished. On the other hand, as a true believer, you're concerned with fixing on a particular conception of human knowledge as justified true belief.

For example, William Bartley developed the concept of justificationsm from Karl Popper’s criticism of the authoritarian strand in western epistemology and political theory. David Deutsch developed his concept of hard to vary explanations based on criticism of Popper's criterion of falsification (see http://www.ecclectica.ca/issues/2003/1/lewthwaite.asp), etc.

In other words, we're not going to make any progress until you realize that you're trying to compare apples and oranges.

Scott said" unable to recognize your conception of human knowledge as an idea that would be subject to criticism. "

No Scott, I`m perfectly aware that human knowledge should be subject of criticism. Are you that do not understand that before the criticism there is already human knowledge, and that criticism itself is a process of the human knowledge.The problem is you do not have rational hypotesys for how this knowledge come from.Yes I`m talking about apples and you answer oranges without realizing it.

Blas: No Scott, I'm perfectly aware that human knowledge should be subject of criticism.

That's the thing, Blas. When I say you hold a pre-enlightenment, justificationist, authoritative conception of human knowledge", I'm not referring to the contents of human knowledge. Rather, I'm taking conceptions of what knowledge is and how humans acquire it.

So, it seems you still unable to recognize your conception of human knowledge as an idea that would be subject to criticism.

"I'm not referring to the contents of human knowledge. Rather, I'm taking conceptions of what knowledge is and how humans acquire it."

Scott try to forget for a minute your dogmativ view and try to understand what I`m saying.

What knowledge is is a knowledge content.How we acquire knowledge is a knowledge contentSo you are referring to the contents of knowledge.You keep repeating that knowledge is acquired by testing and crtizicing hypothesys. I tell you hypothesys are already knowledge and for critizicing them you need more knowledge. My question is where this knowledge come frome in order to allow us crticize it?

CH said, "In other words, results that rebuke a fundamental concept of evolution, and that cannot even be explained by evolutionists (who are notorious for being able to explain anything with their just-so stories), are presented by evolutionists as important findings for understanding how evolution works."

Yes because evolution is a fact like gravity. Gravity is a fact because we can observe it and measure it. Like a ball falling off a 10 story building. Evolution is a fact because we can observe bird beaks and guppies and everything else not evolving. Evolution is a fact because we can interpret a fossil record with marvelously new forms of life abruptly appearing in the record followed by stasis and extinction.

Speciation can't be observed because evolution works too slowly for one lifetime to observe it. Apparently 50,000 generations of Lenski's bacteria is not enough time either. Evolution always has a defense. Its only limitation is not science, but the ability of its supporters to engage in creative story telling.

Evidence for evolution is never straight forward. It must always be defended with speculation rooted in assumption. It is not a hard science, but a philosophy of interpreting data from a narrow metaphysical viewpoint. It elevates willy nilly story telling to dogma. It never apologizes for its errors, it excuses and accuses. It fights strawmen. It's a pretend world. Like a movie. The characters aren't real. Evolutionists live in this world of make believe. It elevates nature by exaggerating its potential. It's superstition. Every now and then a outside knock is heard telling them that there is a real world outside that contradicts their world, but they just turn up the volume and go on pretending.

Neal: CH said, "In other words, results that rebuke a fundamental concept of evolution, and that cannot even be explained by evolutionists (who are notorious for being able to explain anything with their just-so stories), are presented by evolutionists as important findings for understanding how evolution works."

Yes because evolution is a fact like gravity.

The theory of evolution is not "a fact like gravity". Evolution, as defined as "change in allele frequency over time" or even as "change allele frequency over time in favour of traits that confer greater reproductive success in the current environment", however, is a fact like "massive objects attract each other.

In other words, both are observations.

Gravity is a fact because we can observe it and measure it.

We can observe and measure mass, and we can observe that massive objects attract each other. We call this attractive property of mass "gravity" just as can measure change in allele frequency over time, and call it "evolution". But the gravity is no more, and no less, a "fact" than "evolution" is - both are names we give to something that occurs predictably.

But we do not know how gravity works. There is no actual explanatory theory of gravity, just a set of equations that hold with law-like consistency with our observations.

Evolutionary theory, however, really is a theory - it actually explains what we observe. It's a theory well supported by evidence, and so many people, it seems, like to refer to it as a "fact", just as we regard it as a "fact" that germs cause disease. But the germ theory of disease is only a "fact" in the sense that the theory of evolution is a "fact".

Gravity, however, is simply a "fact": it's the the name we give to an observational law.

Like a ball falling off a 10 story building. Evolution is a fact because we can observe bird beaks and guppies and everything else not evolving.

We observe them evolving (i.e. their allele frequencies change over time, and are biased in favour of traits that promote reproductive success in the current environment) and those observations are facts.

Evolution is a fact because we can interpret a fossil record with marvelously new forms of life abruptly appearing in the record followed by stasis and extinction.

No, but that fossil record is a vast set of facts that support the theory of evolution very well.

Speciation can't be observed because evolution works too slowly for one lifetime to observe it.

No, we can observe it, but we cannot observe irreversible speciation in one lifetime, nor in many.

Apparently 50,000 generations of Lenski's bacteria is not enough time either.

That's becase bacteria don't actually speciate. But we certainly see new strains evolving to thrive in a new environment. Lenski observed this, and it is of course also a problem for human health.

Evolution always has a defense. Its only limitation is not science, but the ability of its supporters to engage in creative story telling.

It certainly has a defense against arguments like these, Neal, which are either attacks on a straw man, or simply misinformed.

Evidence for evolution is never straight forward. It must always be defended with speculation rooted in assumption.

This is mere well-poisoning. Evidence for evolution is as straightforward as evidence for any theory - you systematically test hypotheses.

It is not a hard science, but a philosophy of interpreting data from a narrow metaphysical viewpoint.

Neal Tedford: Speciation can't be observed because evolution works too slowly for one lifetime to observe it. Apparently 50,000 generations of Lenski's bacteria is not enough time either.

Speciation is not well-defined for bacteria. (You should know that by now.) However, substantial evolutionary changes were observed by Lenski and his team. That's why we can say evolution is a fact. Also, because there is evolution, there is an evolutionary history. When we combine these facts with other facts, such as the nested hierarchy and fossil succession, we can infer many aspects of this history.

'However, substantial evolutionary changes were observed by Lenski and his team. That's why we can say evolution is a fact."

And yet the reality knocking at the Darwinian door of fantasy states:

Richard Lenski’s Long-Term Evolution Experiments with E. coli and the Origin of New Biological Information – September 2011Excerpt: The results of future work aside, so far, during the course of the longest, most open-ended, and most extensive laboratory investigation of bacterial evolution, a number of adaptive mutations have been identified that endow the bacterial strain with greater fitness compared to that of the ancestral strain in the particular growth medium. The goal of Lenski’s research was not to analyze adaptive mutations in terms of gain or loss of function, as is the focus here, but rather to address other longstanding evolutionary questions. Nonetheless, all of the mutations identified to date can readily be classified as either modification-of-function or loss-of-FCT.(Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010).)http://www.evolutionnews.org/2011/09/richard_lenskis_long_term_evol051051.html

Mutations : when benefits level off – June 2011 – (Lenski’s e-coli after 50,000 generations)Excerpt: After having identified the first five beneficial mutations combined successively and spontaneously in the bacterial population, the scientists generated, from the ancestral bacterial strain, 32 mutant strains exhibiting all of the possible combinations of each of these five mutations. They then noted that the benefit linked to the simultaneous presence of five mutations was less than the sum of the individual benefits conferred by each mutation individually.http://www2.cnrs.fr/en/1867.htm?theme1=7

"The neo-Darwinians would like us to believe that large evolutionary changes can result from a series of small events if there are enough of them. But if these events all lose information they can’t be the steps in the kind of evolution the neo-Darwin theory is supposed to explain, no matter how many mutations there are. Whoever thinks macroevolution can be made by mutations that lose information is like the merchant who lost a little money on every sale but thought he could make it up on volume." Lee Spetner (Ph.D. Physics - MIT - Not By Chance)

‘Darwinian evolution is impossible’ - John Sanford - Geneticist‘Mutations are word-processing errors in the cell’s instruction manual. Mutations systematically destroy genetic information—even as word processing errors destroy written information. While there are some rare beneficial mutations (Even the rare beneficial mutations still lose information), bad mutations outnumber them—perhaps by a million to one. So even allowing for beneficial mutations, the net effect of mutation is overwhelmingly deleterious. The more the mutations, the less the information. This is fundamental to the mutation process.’http://creation.com/geneticist-evolution-impossible

bornagain77: "But if these events all lose information they can’t be the steps in the kind of evolution the neo-Darwin theory is supposed to explain, no matter how many mutations there are. Whoever thinks macroevolution can be made by mutations that lose information is like the merchant who lost a little money on every sale but thought he could make it up on volume"

Yes, we're aware of the claim. Please provide an unambiguous metric of "information".

Measuring the functional sequence complexity of proteins - Kirk K Durston, David KY Chiu, David L Abel and Jack T Trevors - 2007Excerpt: We have extended Shannon uncertainty by incorporating the data variable with a functionality variable. The resulting measured unit, which we call Functional bit (Fit), is calculated from the sequence data jointly with the defined functionality variable. To demonstrate the relevance to functional bioinformatics, a method to measure functional sequence complexity was developed and applied to 35 protein families.,,,http://www.tbiomed.com/content/4/1/47

Three subsets of sequence complexity and their relevance to biopolymeric information - Abel, TrevorsExcerpt: Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC).,,, Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,,

Testable hypotheses about FSC

What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses:

Null hypothesis #4Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time.

We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified.http://www.tbiomed.com/content/2/1/29

It is interesting to point out that information is transcendent of any material basis. That is to say that although information can be encoded onto various material substrates the information is NOT the material substrate. i.e. the music on a CD or iPod is NOT the CD or iPod. And although no one has ever seen material processes producing transcendent functional information, neo-Darwinists insist that the the stunning levels of massively integrated functional information we find in life, which our best computer programmers can only drool over, arose by purely material processes. This is simply 'not even wrong'. First, on top of the fact no one has ever witnessed material processes generating functional information, is the fact that 'material' (mass and photons) is now shown to reduce to transcendent information in quantum teleportation experiments. Second is that classical information, such as the functional information we see programmed into computers and into life, is now shown to be a subset of quantum information by the following proof:

Quantum knowledge cools computers: New understanding of entropy – June 2011Excerpt: The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. http://www.sciencedaily.com/releases/2011/06/110601134300.htm

,,,And to dot the i’s, and cross the t’s, here is the empirical confirmation that quantum information is in fact ‘conserved’;,,,

Quantum no-hiding theorem experimentally confirmed for first timeExcerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment.http://www.physorg.com/news/2011-03-quantum-no-hiding-theorem-experimentally.html

Thus it is simply ludicrous for neo-Darwinists to insist transcendent (beyond space and time) information can arise by purely material processes when material processes are shown to be 'bottom rung of the ladder' as far as reality itself is structured towards information!

John 1 1-5In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. In him was life, and that life was the light of all mankind. The light shines in the darkness, and the darkness has not overcome it.

Zach, perhaps instead of using a 'man-made' protein that inhibited functionality of a living cell by 'gumming up the works' you would care to present a truly functional protein, that actually does something useful in the cell, besides inhibiting functionality, that was arrived at by purely material, neo-Darwinian, processes? Or is the fact that you have to use a 'man-made' protein indicative of the fact that you have no examples of functional proteins being arrived at by purely material neo-Darwinian processes??? Oh well,,

But to be fair, let's use a common protein domain:

"Let’s be simple. Durston measures the functional information in the P 53 DNA domain at 525 Fits. Therefore, according to my definition and threshold, and even according to Dembski’s threshold, it is a protein which can be classified as exhibiting dFSCI. That means that a purely random search, starting form any non related starting state, be it from scratch of form an existing unrelated sequence, has to generate 525 bits of functional information to produce that protein domain.

Now, if you or anyone else has a gradual model for the origin of that protein domain, please give it. If you believe that there are functional selectable intermediates, please tell us what they can be, and why they were selected. We then will restrict the analysis to the random transitions in your model." - gppucio - UD blogger - MDhttp://www.uncommondescent.com/intelligent-design/why-secular-and-theistic-darwinists-fear-id/#comment-363540

Note: Zach, p53 instead of gumming up the works as your man-made example does, is a example of 'poly-functionality that has greatly exceeded human expectation and understanding:

The p53 network she spoke of is a good example of unexpected complexity. Discovered in 1979, the p53 protein was first thought to be a cancer promoter, then a cancer suppressor. “Few proteins have been studied more than p53,” she said. “...Yet the p53 story has turned out to be immensely more complex than it seemed at first.” She gave some details:

Researchers now know that p53 binds to thousands of sites in DNA, and some of these sites are thousands of base pairs away from any genes. It influences cell growth, death and structure and DNA repair. It also binds to numerous other proteins, which can modify its activity, and these protein–protein interactions can be tuned by the addition of chemical modifiers, such as phosphates and methyl groups. Through a process known as alternative splicing, p53 can take nine different forms, each of which has its own activities and chemical modifiers. Biologists are now realizing that p53 is also involved in processes beyond cancer, such as fertility and very early embryonic development. In fact, it seems wilfully [sic] ignorant to try to understand p53 on its own. Instead, biologists have shifted to studying the p53 network, as depicted in cartoons containing boxes, circles and arrows meant to symbolize its maze of interactions. http://creationsafaris.com/crev201004.htm#20100405a

bornagain: perhaps instead of using a 'man-made' protein that inhibited functionality of a living cell by 'gumming up the works'

There's nothing in your citation that mentions artificial proteins are excluded from the measure. They talk about molecular function, and binding is one of the primary molecular functions, along with ligasing and lyases.

Zach, and I'm suppose to take your gross distortion of the evidence seriously because??? because??? because you desperately want Darwinism to be true??? Sorry padre no exceptions for your religious preference just because it doesn't match reality! i.e. no rationalizations need apply!

Functional information and the emergence of bio-complexity:Robert M. Hazen, Patrick L. Griffin, James M. Carothers, and Jack W. Szostak:Abstract: Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define 'functional information,' I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA-GTP binding energy), I(Ex)= -log2 [F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function > Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of functions.http://genetics.mgh.harvard.edu/szostakweb/publications/Szostak_pdfs/Hazen_etal_PNAS_2007.pdf

Here is another paper Zach, a paper that is right down your alley. Even though the findings have nothing of "evolutionary significance' to report, in fact the findings have Intelligent Design written all over them, the article none the less pays homage to evolution in the title:

Despite what the title says, there is nothing evolutionarily significant about this following finding

Protein knots gain new evolutionary significance - June 5, 2012 Excerpt: "The presence of a knotted or slipknotted structure in a protein is relatively rare but really is very interesting," said Kenneth Millett, a professor of mathematics at UC Santa Barbara and a co-author of the paper, "Conservation of complex knotting and slipknotting patterns in proteins," published in the Proceedings of the National Academy of Sciences.Relatively little is known about protein folding, the process by which a polypeptide chain with a specific sequence of amino acid chains forms the three-dimensional structures — their "native states" — required to become functional. How this process reproducibly achieves the required structure is the subject of intensive study. Even harder is understanding how this is accomplished for knotted proteins, where the chain loops around itself in entanglements of varying complexity; or the even rarer slipknotted proteins, where a loop is bound by another segment of the protein chain, similar to a shoelace bow. ""These knots may help to identify features that turn out to be important, and aspects of the structure that are more generalizable. We need to clearly understand how these things come to be, what are the implications of their structure, and how might one be able to somehow guide them," said Millett.http://phys.org/news/2012-06-protein-gain-evolutionary-significance.html

Keefe & Szotak: I read some of the prep for this research. What does, "was specifically constructed to avoid stop codons and frameshift mutations, and was designed for use in mRNA display selections" and, "we selected functional proteins by enriching for those that bind to ATP" mean?

The words I don't understand in these two sentences are "designed" and "specifically constructed"...as well as "we selected".

"Bornagain77 is the one making the claim about information."

Could you please explain exactly what you mean by measure of information.

There's creating a library of random proteins of a given length. If you want to make random sentences of a given length, you would avoid periods, that is, stop codons. Frameshifts during synthesis also introduces stop codons, which would truncate the sequence.

ForJah: "and was designed for use in mRNA display selections"

The RNA molecule that produces the protein is chemically bound to the protein. You can think of it as a tag that can be recovered later to identify the sequence.

ForJah: "we selected functional proteins by enriching for those that bind to ATP" mean?

The function of interest was ATP-binding. If a given protein binds to ATP, it is selected for replication, while the others are discarded. This process is repeated a number of times.

ForJah: The words I don't understand in these two sentences are "designed" and "specifically constructed"

That is in reference to creating the library of random sequences.

ForJah: ...as well as "we selected".

They were looking for proteins that bind to ATP, so those are the ones they selected. There were several rounds of selection, which increased the function, but some of the original random sequences bound to ATP, albeit weakly.

ForJah: Could you please explain exactly what you mean by measure of information.

We haven't made any claims about a measure of information. There are several measures that we would be happy to consider (e.g. Shannon Entropy or Kolmogorov Complexity), as long as the measure is specific, unambiguous, and can be calculated for every element of the relevant category.

Wow, you are very good at this stuff! The only thing I think I'm caught up on is how is this research analogous with nature? Selecting and discarding functional proteins requires the intelligence of the researchers...so how can you appeal to this study to show how proteins develop by chance? As I understand it, proteins do not self-replicate. I am not very fluent in biology or information theory but I know the general ideas so excuse me if I'm missing something.

Okay sounds good...what I'm about to link is all gibberish to me, even though i took High level calc, but since education in America sucks, I forgot it all now. I'm not really sure if it is relevant but I figured I'd give it a shot.

Zachriel said “Not unexpectedly. Remember, Niels only has to outrun Albert, not the bear.”

Morning commute thinking produced slightly different version:

Nature doesn’t care

Who gets eaten by the bear

That seems to be the mechanism at work in the nature. Goes hand in hand with the “selfish gene” idea. Dawkins wrote the Selfish Gene, I must say I don’t get the idea. That’s another story.

If life started by pure natural process it should stay simple and only direction in development should be simplicity, robustness, survivability, “selfishness”. Life should be “tuned “via RM+NS only. It would avoid unnecessary complications at any cost. The Price Is Right has a game where contestant has to say “That’s too much!” when guessing price of the car.

I would expect Nature to have a very low threshold for complications that seem to be built into living things. It would call “That’s too much!” very early.

,,,Michael Behe defends the one 'overlooked' protein/protein binding site generated by the HIV virus, that Abbie Smith and Ian Musgrave had found, by pointing out it is well within the 2 binding site limit he set in "The Edge Of Evolution" on this following site:

Response to Ian Musgrave's "Open Letter to Dr. Michael Behe," Part 4 "Yes, one overlooked protein-protein interaction developed, leading to a leaky cell membrane --- not something to crow about after 10^20 replications and a greatly enhanced mutation rate." http://behe.uncommondescent.com/page/4/

An information-gaining mutation in HIV? NO!http://creation.com/an-information-gaining-mutation-in-hiv

In fact, I followed this debate very closely and it turns out the trivial gain of just one protein-protein binding site being generated for the non-living HIV virus, that the evolutionists were 'crowing' about, came at a staggering loss of complexity for the living host it invaded (People) with just that one trivial gain of a 'leaky cell membrane' in binding site complexity. Thus the 'evolution' of the virus clearly stayed within the principle of Genetic Entropy since far more functional complexity was lost by the living human cells it invaded than was ever gained by the non-living HIV virus. A non-living virus which depends on those human cells to replicate in the first place. Moreover, while learning HIV is a 'mutational powerhouse' which greatly outclasses the 'mutational firepower' of the entire spectrum of higher life-forms combined for millions of years, and about the devastating effect HIV has on humans with just that one trivial binding site being generated, I realized if evolution were actually the truth about how life came to be on Earth then the only 'life' that would be around would be extremely small organisms with the highest replication rate, and with the most mutational firepower, since only they would be the fittest to survive in the dog eat dog world where blind pitiless evolution rules and only the 'fittest' are allowed to survive.

Eugen: I would expect Nature to have a very low threshold for complications that seem to be built into living things.

Well, your expectation is contradicted by the plain facts. Multicellular organisms may not be as numerous as bacteria, but have been evolutionarily successful for hundreds of millions of years, and can be observed successfully reproducing even today.

i.e. that 'global transformation' is clearly a 'design' expectation, not a survival of the fittest Darwinian expectation!

The fine-tuning of bacterial life to higher life is simply astonishing:

Engineering and Science Magazine - Caltech - March 2010Excerpt: “Without these microbes, the planet would run out of biologically available nitrogen in less than a month,” Realizations like this are stimulating a flourishing field of “geobiology” – the study of relationships between life and the earth. One member of the Caltech team commented, “If all bacteria and archaea just stopped functioning, life on Earth would come to an abrupt halt.” Microbes are key players in earth’s nutrient cycles. Dr. Orphan added, “...every fifth breath you take, thank a microbe.”http://www.creationsafaris.com/crev201003.htm#20100316a

Planet's Nitrogen Cycle Overturned - Oct. 2009Excerpt: "Ammonia is a waste product that can be toxic to animals.,,, archaea can scavenge nitrogen-containing ammonia in the most barren environments of the deep sea, solving a long-running mystery of how the microorganisms can survive in that environment. Archaea therefore not only play a role, but are central to the planetary nitrogen cycles on which all life depends.,,,the organism can survive on a mere whiff of ammonia – 10 nanomolar concentration, equivalent to a teaspoon of ammonia salt in 10 million gallons of water."http://www.sciencedaily.com/releases/2009/09/090930132656.htm

The bear certainly has a say in who gets ate, slower runner,less energy expended,better survival odds bear wise.And probably Albert is fatter ,as well as slower, so it is a win/ win for the bear and nature.

At Brazos Bend Park alligators provide the incentive to be not the slowest in your group,or the stupidest.

Not really foresight, if you don't know ahead of time that there is a problem. They are in the present,do you think the cells have a sense of time? They solve it by mutations,if they change something that give any advantage givien enough time they win,the reason the house wins in Vegas ,if not they get ate by the bear.

Atheistic neo-Darwinists claim that given enough time the improbable becomes probable. i.e. Evolution, no matter how improbable, becomes certain if you allow enough time according to their reasoning. Thus to counter such simplistic reasoning in the power of time to work miracles, here are a few notes to the contrary of what the neo-Darwinists take on blind faith in the power of time;

William Lane Craig - If Human Evolution Did Occur It Was A Miracle - videohttp://www.youtube.com/watch?v=GUxm8dXLRpA

In Barrow and Tippler’s book The Anthropic Cosmological Principle, they list ten steps necessary in the course of human evolution, each of which, is so improbable that if left to happen by chance alone, the sun would have ceased to be a main sequence star and would have incinerated the earth. They estimate that the odds of the evolution (by chance) of the human genome is somewhere between 4 to the negative 180th power, to the 110,000th power, and 4 to the negative 360th power, to the 110,000th power. Therefore, if evolution did occur, it literally would have been a miracle and evidence for the existence of God.William Lane Craig

A review of The Edge of Evolution: The Search for the Limits of DarwinismExcerpt: The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155).http://creation.com/review-michael-behe-edge-of-evolution

Waiting Longer for Two Mutations – Michael J. BeheExcerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that ‘for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years’ (1 quadrillion years)(Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘is 5 million times larger than the calculation we have just given’ using their model (which nonetheless “using their model” gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model.http://www.discovery.org/a/9461

The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway – Ann K. Gauger and Douglas D. Axe – April 2011Excerpt: We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions. But evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth.http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.1/BIO-C.2011.1

When Theory and Experiment Collide — April 16th, 2011 by Douglas AxeExcerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.http://biologicinstitute.org/2011/04/16/when-theory-and-experiment-collide/

bornagain77: Atheistic neo-Darwinists claim that given enough time the improbable becomes probable. i.e. Evolution, no matter how improbable, becomes certain if you allow enough time according to their reasoning.

Darn those "atheistic neo-Darwinists, whomever they are! But scientists believe that evolutionary trajectories are well within what is expected by the time allowed. One of the original predictions of Darwin's theory, that the Earth was much older than what the physicists allowed. On the other hand, evolutionary theory predicts that observed rates of evolution must be at least as fast as the fastest rate inferred from the historical record. Observed rates are many times faster.

bornagain77: The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution.

They eat human children, despite the best technological efforts of humans. From the point of view of the Plasmodia, that's a significant achievement. Better luck next time.

Book Review – Meyer, Stephen C. Signature in the Cell. New York: HarperCollins, 2009.Excerpt: As early as the 1960s, those who approached the problem of the origin of life from the standpoint of information theory and combinatorics observed that something was terribly amiss. Even if you grant the most generous assumptions: that every elementary particle in the observable universe is a chemical laboratory randomly splicing amino acids into proteins every Planck time for the entire history of the universe, there is a vanishingly small probability that even a single functionally folded protein of 150 amino acids would have been created. Now of course, elementary particles aren’t chemical laboratories, nor does peptide synthesis take place where most of the baryonic mass of the universe resides: in stars or interstellar and intergalactic clouds. If you look at the chemistry, it gets even worse—almost indescribably so: the precursor molecules of many of these macromolecular structures cannot form under the same prebiotic conditions—they must be catalysed by enzymes created only by preexisting living cells, and the reactions required to assemble them into the molecules of biology will only go when mediated by other enzymes, assembled in the cell by precisely specified information in the genome.So, it comes down to this: Where did that information come from? The simplest known free living organism (although you may quibble about this, given that it’s a parasite) has a genome of 582,970 base pairs, or about one megabit (assuming two bits of information for each nucleotide, of which there are four possibilities). Now, if you go back to the universe of elementary particle Planck time chemical labs and work the numbers, you find that in the finite time our universe has existed, you could have produced about 500 bits of structured, functional information by random search. Yet here we have a minimal information string which is (if you understand combinatorics) so indescribably improbable to have originated by chance that adjectives fail.http://www.fourmilab.ch/documents/reading_list/indices/book_726.html

Archaean Microfossils and the Implications for Intelligent Design – August 2011Excerpt: This dramatically limits the amount of time, and thus the probablistic resources, available to those who wish to invoke purely unguided and purposeless material processes to explain the origin of life.http://www.evolutionnews.org/2011/08/surprisingly_soon_archaean_mic049921.html

Without enzyme, biological reaction essential to life takes 2.3 billion years: UNC study:In 1995, Wolfenden reported that without a particular enzyme, a biological transformation he deemed “absolutely essential” in creating the building blocks of DNA and RNA would take 78 million years.“Now we’ve found a reaction that – again, in the absence of an enzyme – is almost 30 times slower than that,” Wolfenden said. “Its half-life – the time it takes for half the substance to be consumed – is 2.3 billion years, about half the age of the Earth. Enzymes can make that reaction happen in milliseconds.”http://www.med.unc.edu/www/newsarchive/2008/november/without-enzyme-biological-reaction-essential-to-life-takes-2-3-billion-years-unc-study

“Phosphatase speeds up reactions vital for cell signalling by 10^21 times. Allows essential reactions to take place in a hundreth of a second; without it, it would take a trillion years!” Jonathan Sarfatihttp://www.pnas.org/content/100/10/5607.abstract

Not only do we not have enough time for Darwinian evolution, we don’t, as massive as it is, even have a big enough universe for Darwinian evolution:

Abiogenic Origin of Life: A Theory in Crisis – Arthur V. Chadwick, Ph.D.Excerpt: The synthesis of proteins and nucleic acids from small molecule precursors represents one of the most difficult challenges to the model of prebiological evolution. There are many different problems confronted by any proposal. Polymerization is a reaction in which water is a product. Thus it will only be favored in the absence of water. The presence of precursors in an ocean of water favors depolymerization of any molecules that might be formed. Careful experiments done in an aqueous solution with very high concentrations of amino acids demonstrate the impossibility of significant polymerization in this environment. A thermodynamic analysis of a mixture of protein and amino acids in an ocean containing a 1 molar solution of each amino acid (100,000,000 times higher concentration than we inferred to be present in the prebiological ocean) indicates the concentration of a protein containing just 100 peptide bonds (101 amino acids) at equilibrium would be 10^-338 molar. Just to make this number meaningful, our universe may have a volume somewhere in the neighborhood of 10^85 liters. At 10^-338 molar, we would need an ocean with a volume equal to 10^229 universes (100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000) just to find a single molecule of any protein with 100 peptide bonds. So we must look elsewhere for a mechanism to produce polymers. It will not happen in the ocean.http://origins.swau.edu/papers/life/chadwick/default.html

Protein Life Times: Just-Right Evidence for Design - Fazale Rana PhD. biochemistryExcerpt: A few years ago, researchers discovered that when proteins become denatured and unfold, they expose stretches of amino acids (called a hydrophobic β–sheet structure) that possess a strong tendency to clump with other like sequences. Normally, these sequences are buried deep within the interior of the folded protein and can’t come into contact with corresponding sequences in other proteins. It’s only when proteins become denatured and either partially or completely unfold that these aggregation-promoting sequences are exposed to other proteins, exerting their deleterious effects.But researchers also discovered amino acid residues adjacent to the hydrophobic β–sheet sequences that disrupt protein aggregation.2 These aggregation-reducing amino acids are called “gate-keeping” residues. It turns out that strongly aggregating sequences are flanked by more gate-keeping residues than those that are weakly aggregating. Proteins’ amino acid sequences appear carefully designed to minimize aggregation.3

…And Optimized to Ensure Structural Stability

But a trade-off exists. The strongly aggregating sequences are necessary to stabilize proteins when they fold into their naturally intended three-dimensional shapes. Researchers learned that the amino acid sequences are exquisitely arranged to precisely balance the need for structural stability, while minimizing aggregation propensity.,,,Yet the optimization of proteins is not limited to their aggregation propensities. A cascade of optimization characterizes protein structure and function. In The Cell’s Design, I described a number of other ways that protein structure is optimized.http://www.reasons.org/articles/protein-life-times-just-right-evidence-for-design

Exactly! They appear carefully designed. The same appearance of design that goes back at least as far as William Paley. The only difference is that neo-Paleyists like Rana can see much deeper into the structure of living things than was possible in Paley's day - thanks largely to the work of evolutionary biologists.

But while the field of evolutionary biology is flourishing as researchers build on Darwin's seminal work, in the same period, neo-Paleyists have not advanced our knowledge of the Designer one bit.

Actually Ian it is interesting to bring up Paley, for, as you pointed out, Paley did not have the advantage of electron microscopes, knowledge of the absurd levels of information programming in cells, molecular machines etc.. that we have today. Paley's watchmake analogy is magnitudes of orders stronger than it was in Paley's day. In fact, serendipitously, this article just came out the other day pointing out that very fact:

Do Biological Clocks Revive William Paley's Design Argument? - June 2012Excerpt: A primary criticism of William Paley's "watchmaker argument" for a designer is that organisms are vastly different from man-made machines. What then should we say about ongoing discoveries of mechanisms in living cells that not only keep time, but do it more elegantly than anything man has invented?,,, Another paper in Science from October 31, 2008 actually spoke of cogs and gears in biological clocks -- of bacteria!http://www.evolutionnews.org/2012/06/do_biological_c060411.html

further notes:

Paley’s Watch Found in BacteriaThe conjunction of structural, biophysical, and biochemical approaches to this system reveals molecular mechanisms of biological timekeeping. http://creationsafaris.com/crev200810.htm#20081031a

Clockwork That Drives Powerful Virus Nanomotor DiscoveredExcerpt: Because of the motor's strength--to scale, twice that of an automobile--the new findings could inspire engineers designing sophisticated nanomachines.http://www.sciencedaily.com/releases/2008/12/081229200748.htm

Molecular Motors In Cells Work Together, Study ShowsExcerpt: "We found that molecular motors operate in an amazingly coordinated manner when moving an algal cell one way or the other,"http://www.sciencedaily.com/releases/2009/02/090213161043.htm

Pulsating Response to Stress in Bacteria Discovered - (Nov. 3, 2011)Excerpt: The bacterial gene circuit amplifies these molecular fluctuations, also called noise, to generate discrete pulses of σB activation. The stress also activates another key protein that modulates the pulse frequencies.By turning a steady input (the stress) into an oscillating output (the activation of σB) the genetic circuit is analogous to an electrical inverter, a device that converts direct current (DC) into alternating current (AC), explains Michael Elowitz, professor of biology and bioengineering at Caltech, Howard Hughes Medical Institute investigator, and coauthor of the paper. "You might think you need some kind of elaborate circuitry to implement that, but the cell can do it with just a few proteins, and by taking advantage of noise.",,, "With this work and recent work in other systems, we're starting to get a glimpse of just how dynamic cellular control systems really are," Elowitz adds. "That's something that was very difficult to see in the past."http://www.sciencedaily.com/releases/2011/11/111103120607.htm

Ian since the only other watches I've ever seen are made by intelligence, and neo-Darwinian processes certainly have never been observed to generate ANY molecular machine, including any clocks, or time-keeping mechanisms, why am I to presuppose blind material processes as the reason why these machines originated? It simply defies sanity to insist as such!

Actually Ian it is interesting to bring up Paley, for, as you pointed out, Paley did not have the advantage of electron microscopes, knowledge of the absurd levels of information programming in cells, molecular machines etc.. that we have today. Paley's watchmake analogy is magnitudes of orders stronger than it was in Paley's day.

No, just like seeing the face of Christ in a damp stain on a wall, it's the same old false-positive it always was. The only difference is that we can now see them at the molecular level.

Ian since the only other watches I've ever seen are made by intelligence, and neo-Darwinian processes certainly have never been observed to generate ANY molecular machine, including any clocks, or time-keeping mechanisms, why am I to presuppose blind material processes as the reason why these machines originated? It simply defies sanity to insist as such!

The only watches any of us have ever seen were made by us. We have no idea what alien design might look like, even if we would recognize it as such. But even if you were to find evidence of alien intervention in the course of life on Earth, wonderful as that would be, it still just pushes the question of origins back one stage. We would then ask how the aliens originated.

And, no, we haven't seen "molecular machines" generated by neo-Darwinian processes in our lifetime. But why would you expect to if such processes are supposed to take tens or hundreds of thousands of years to happen?

In answer to your last question, I would ask the opposite of you. Why should anyone presuppose the existence of a neo-Paleyist designer? No such being has ever been observed. The only evidence - if you can call it that - for such a being is the appearance of design in Nature and the unverifiable claims of some religious texts.

Actually Ian, until you or any other atheistic neo-Darwinist can prove that purely material processes can generate functional information (Abel; Null Hypothesis) and/or molecular machines (Behe: Darwin's Black Box) then Intelligent Design is, by far, the most causally adequate explanation for how the information and machines got there. For you to insist otherwise is to ignore the very same method of science that Darwin himself used to reason for evolution in the first place! You don't want to be 'unscientific' do you? (as if atheism could ground science)

Intelligent Design is vacuous as an explanation. Its proponents refuse to be drawn on the identity of the Designer (although we all know Who it is really), the nature of this Designer, the powers of this Designer or how it brought about its designs. All we have in effect is a label, a placeholder for an explanation that dare not speak its name and is utterly inadequate causally.

Ian small correction, "Neo-Darwinism is vacuous as an explanation. Its proponents refuse to be drawn on the identity of the random chance (although we all know What it is really), the nature of this random chance, the powers of this random chance or how random chance brought about its designs. All we have in effect is a label, a placeholder for an explanation that dare not speak its name and is utterly inadequate causally.

There Ian, all better now!

Further notes:

Evolution and the Illusion of Randomness - Talbott - Fall 2011Excerpt: The situation calls to mind a widely circulated cartoon by Sidney Harris, which shows two scientists in front of a blackboard on which a body of theory has been traced out with the usual tangle of symbols, arrows, equations, and so on. But there’s a gap in the reasoning at one point, filled by the words, “Then a miracle occurs.” And the one scientist is saying to the other, “I think you should be more explicit here in step two.”In the case of evolution, I picture Dennett and Dawkins filling the blackboard with their vivid descriptions of living, highly regulated, coordinated, integrated, and intensely meaningful biological processes, and then inserting a small, mysterious gap in the middle, along with the words, “Here something random occurs.”This “something random” looks every bit as wishful as the appeal to a miracle. It is the central miracle in a gospel of meaninglessness, a “Randomness of the gaps,” demanding an extraordinarily blind faith. At the very least, we have a right to ask, “Can you be a little more explicit here?”http://www.thenewatlantis.com/publications/evolution-and-the-illusion-of-randomness

Nobel Prize-Winning Physicist Wolfgang Pauli on the Empirical Problems with Neo-Darwinism - Casey Luskin - February 27, 2012Excerpt: "In discussions with biologists I met large difficulties when they apply the concept of 'natural selection' in a rather wide field, without being able to estimate the probability of the occurrence in a empirically given time of just those events, which have been important for the biological evolution. Treating the empirical time scale of the evolution theoretically as infinity they have then an easy game, apparently to avoid the concept of purposesiveness. While they pretend to stay in this way completely 'scientific' and 'rational,' they become actually very irrational, particularly because they use the word 'chance', not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word 'miracle.'" Wolfgang Pauli (pp. 27-28) -http://www.evolutionnews.org/2012/02/nobel_prize-win056771.html

You are certainly confused on this point. Mutations have causes, such as errors during replication, or due to radiation. What is meant by random is that the mutations are uncorrelated with fitness. There is substantial evidence that mutations are random, at least in many cases (Lederberg 1952); though the rate of mutation does seem subject to evolutionary constraints, and even varies across the genome.

your metaphor is not clear. By the way if one of the steps (e.g. "simple self replicating molecules") is reached the following one (e.g. "small organisms") is more likely to be achieved. Indirectly you are suggesting that Nature's "preference" is to "evolve" from 1 to 4.

Yes “care” is a metaphor left from convenient rhyme bear-care which started with Zachriel’s funny bear chasing Albert and Neils.

Natural process is indifferent to its outcomes. It has no goals, any event is as likely as any other one. I think Nature left alone would produce nothing. By some miraculous series of chance events it would produce a few simple molecules, which may replicate and than what?

We need another series of miraculous chance events to get to the next level. All along we are hoping the result of the first miracle is not destroyed by random events. I think it’s most likely Nature would stay as close to elementary materials and basic reactions as possible. If anything that would be her goal, simplicity and equilibrium.

OTOH, Kaufman is examining possibilities with his interesting idea of autocatalytic sets. In one of his books (Sacred Reinvented I think) Kaufman mentioned another interesting guy: Ulanowitz and his work in environmental science. I printed some articles by Ulanowitz; they are in queue for reading.These scientists are examining capabilities of nature but don’t seem to be rabid atheists like Dawkins. It’s hard for moderates to listen to extremists like Dawkins and his team. I don’t think the other two people are theists but Kaufman could be borderline. He pretty much invented his own mini natural religion.

We are not sure about that. For planets with volcanos and tornados we still relay on an unverified theory of Kant, that dust would collapse in gravitational nucleus while the universe is expanding.For galaxies we need dark matter and dark energy.So the idea that nature can produce that things left alone is nothing more than a metaphysical framework.

"It takes a long time to get to equilibrium from the Big Bang. It's still an ongoing process."

But that equilibrium is the absolute zero, no movement at all. Not complicated things.

"No. Once you have replicators, then you have competition for resources, meaning evolution."

Blas: If all the universe tend to the no movement, why life try desperatly to avoid it?

You don't have to look to life to see complexity in nature. Supernovas explode, molecules jiggle, ocean waves crash, mountains rise and rain drops fall. These are all emergent phenomena from simple rules of interaction.

Stars and hurricanes forms by accumulation of energy, do not consume, but dissipate this mass energy until they day all that tending to the equilibrium.Life forms by accumulation of mass not related and consume energy to avoid the equilibrium.

Probably the best to say is; there is a doubt that Nature can produce life only on its own.

I watched videos of Dawkins including his debates and interviews. He says all theists are deluded, religions promote killing and other negative stuff. He mocks opponents. Sam Harris otoh seems moderate so is not repulsive like Dawkins. Harris sometimes tries to be too funny during debates to win the audience.All debaters do it more or less, it's probably smart strategy.

But why do you think so? Or is it just a hunch? As Zachriel noted, nature does many weird things all the time.

He says all theists are deluded, religions promote killing and other negative stuff. He mocks opponents.

Given the diversity of religions, most theists must be deluded, and some religions do promote killing. He certainly is mocking, although at close examination, he often comes off as rather tempered. Anyway, I don't like him so much either. Harris' "naturalistic morals" discourse I find to be irritatingly silly.

TBH I don't think we can show direct evidence for supernatural involvement in producing lets say an enzyme. I think it's possible to find clues for that possibility based on our knowledge of complex,organized,regulated and controlled systems we humans can make.

My kids liked show Blues Clues when they were younger. In that show a blue dog surprisingly named Blue, collects clues in her surroundings to help her solve a problem or to understand something new. We are living inside the Cosmic Blues Clues.

Otherwise, I don't think we'll see The Almighty walking down the street wearing sunglasses, sipping ice frapuccino and wearing T shirt "I am who I am". It would be cool,nevertheless. Paparazzi would go crazy....:)

So, if I understand you correctly, to find things that are readily describable in engineering terms hints to an engineering origin for them. If "engineeredness" is to be a useful criterion, one should be able to find some other things that clearly cannot be described in engineering terms. Can you think of any?

If chain of molecules is cut in half so I see two half length chains I should be allowed to use word "cut" instead of a long technical description of the actual chemical reaction which dissociated bonds of the molecular chain.

Electronics

If signal is present at some point in the circuit I should simply say "signal is present" instead of long technical description of movement and accumulation of negative charges along conducting crystalline structures.

This way of thinking helps us modularize complexity into small functional boxes to make it easier to understand basics. After that we can examine what is the relationship between "functional boxes" to have even wider and deeper-system level understanding.

Metaphors are useful for making descriptions of complex things, sure. Specifically, functional talk may help to follow certain sequences of events going on in a system. So what? Your very comment suggests you should be aware of what I perceive to be your biggest mistake, Eugen: metaphor reification. Functions are not things that are there in physical systems. They are subjective descriptions of what's going on in them in relation to some expected result. Have a dishwasher, for example. You can say its function is to clean dishes, and describe how it works to do so. I could say its function is to make water dirty, and I could describe the very same processes that you did. Nothing is different about the physical system itself.

I agree about your warning on metaphor reification. It's hard to stay the middle road between highly technical jargon and metaphors. When I say molecular "chain" is "cut" , I hope to use those words as constructs rather than metaphors.

There is a dilemma. What am I, as a layman supposed to think of name like spliceosome? This "machine" really splices mRNA so its name simply describes the function it performs.

Video was excellent! Only geeks can appreciate how much time goes into those projects. I understand the purpose of showing the video but man, it's too easy to sidetrack me, just show another shiny thing. Please.

I laid my eyes on a new potential project. Problem is with finding time to do it (as usual) Light Cube

I agree about your warning on metaphor reification. It's hard to stay the middle road between highly technical jargon and metaphors.

Hard indeed, many times the jargon itself is made of metaphors. And the are really useful. One has just to keep in mind the difference between metaphors and things themselves.

There is a dilemma. What am I, as a layman supposed to think of name like spliceosome? This "machine" really splices mRNA so its name simply describes the function it performs.

Yes, functional talk is not misleading about the mechanics of the system. It can mislead you into thinking the system has the *purpose* of producing one or another of its many possible effects. That's an entirely different claim that cannot be supported solely by the description of the system. Systems have purposes only in relation to intentional agents, so to support purpose, you must put the system in some context of intentional agents. And that requires external data. So I say, show us the designers first, and then we can start to infer design properly.

This manuscript probably explains it better:ftp://ftp.wehi.edu.au/pub/wilkinsftp/Eliminating_Functions.pdf

Most of what I know about Harris is either second hand or comes from short videos, so I'm not in much of a position to make a defense of him. But knowing natschuster's usual scholarship, I think I'll give him the benefit of the doubt.

He does write in page fifteen of the end of faith that moderate religious people are just as guilty as religious fanatics, and that we cannot tolerate religious beliefs of any kind for that reason. What else can that mean?

And I did some research about tornados and plate techtonics. The stuff about tornados talks about the condition that tornados form under, but not the cause. And I read lots of theory about the causes of plate techtonics, but not a whole lot of facts. And the convection currents that geologiss theorized as a cause of plate techtonics have not been found.